chr21-39825930-T-C

Variant names:

• chr21-39825930-T-C
• rs2837237

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.12 in 152,158 control chromosomes in the GnomAD database, including 1,074 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18280 AN: 152040 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0768

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.120 AC: 18301 AN: 152158 Hom.: 1074 Cov.: 32 AF XY: 0.119 AC XY: 8844 AN XY: 74398

African (AFR) AF: 0.143 AC: 5915 AN: 41504

American (AMR) AF: 0.0994 AC: 1519 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0768 AC: 266 AN: 3462

East Asian (EAS) AF: 0.109 AC: 564 AN: 5166

South Asian (SAS) AF: 0.120 AC: 578 AN: 4816

European-Finnish (FIN) AF: 0.109 AC: 1154 AN: 10608

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7875 AN: 67996

Other (OTH) AF: 0.128 AC: 271 AN: 2114

Alfa AF: 0.115 Hom.: 1596

Bravo AF: 0.122

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2837237; hg19: chr21-41197857;